@Nightvulture I agree with your observation that a lot of cards from around 2000 onward seem to look a bit lighter compared with the earlier WOTC prints.
From what I have seen, Base Set Unlimited 1999 cards and Jungle often have quite strong, darker and more saturated prints overall. Even when the yellow border varies a bit, the actual card colors often still look fairly rich.
With Fossil, especially the non-UK holo prints, I feel like there may be at least two noticeably different looks. Some copies have darker orange-yellow borders and a stronger, more saturated card body/artwork appearance, while others have a lighter yellow border and generally lighter colors across the card with a noticeable difference to Base / Jungle saturation.
Team Rocket seem to be overall lighter compared to Base / Jungle, which fits with the idea that the 2000-era prints can look different from earlier Base/Jungle cards. Their border color saturation does not correlate with the saturation of the artwork or card body in contrast to the Fossil I have seen.
Base Set 2 also seems generally a bit softer and less saturated to me compared with Base Set and Jungle (it also has both dark orange and light yellow border variants which dont seem to correlate with card body saturation).
For the Neo sets, I feel like the whole palette changed compared to Gen 1 prints. The yellow borders often look lighter compared with the Generation 1 WOTC sets, and saturation seems to depend a lot on the individual card color type. Fire and Psychic cards look very strong, while Fighting/Ground or Electric-type cards look comparatively lighter compared to Gen 1 era cards.
Among the Neo-era sets, Neo Discovery in particular feels to me like one of the lighter-looking sets on average. Compared with some other Neo sets, the colors seem much lighter and less saturated on average. Interestingly, the holo bleed variants of Neo Discovery seem to appear darker and more saturated than the regular variants. I wonder if the regular versions may have used a more opaque white layer to reduce the holo effect, which could also make the card body look slightly lighter / less dark.
I also find the WOTC Black Star Promos interesting in that regard. Some promos seem lighter on average, for example Mew #47 compared with Unown J or Misdreavus, while others like Mewtwo #3 or Mewtwo #12 can look extremely saturated.
The Colorless-type promos are also interesting. Dark Persian often seems quite lightly saturated in the card body, almost more white than grey, while Cool Porygon tends to look noticeably darker. Eevee seems to have a particularly wide spread: I have one copy that is very dark, even darker than Cool Porygon, but I’ve also seen copies where the card body looks almost white.
I find that really cool to investigate 
